Studying the macro eco-evolutionary dynamics of birds.
https://claramuntlab.org
Santiago Claramunt
Loading...
I am recruiting a #postdoc to work on assembling and analyzing #genomes of the amazing Furnariidae. Let’s unlock the secret behind their #evolution. The official application portal will be available soon at www.uno.edu/careers. Feel free to contact me for details at [email protected]
Santiago Claramunt
Hey IQTree3 paper is out. Bread and butter for tree building anything in my workflow. They have a pretty standout documentation too.
🖥️🧬
academic.oup.com/mbe/article/...
Female birds with confusing names.
Researchers have identified superparamagnetic macrophages in the livers of rock pigeons to be crucial for magnetic sensing. The finding uncovers an unexpected role for immune cells in sensory perception and may fundamentally change our understanding of animal navigation.
https://scim.ag/4nTQ3nq
Converting images to trees has a long history. @arambaut.bsky.social wrote TreeThief many years ago, @bljog.bsky.social released TreeRipper over a decade ago doi.org/10.1186/1471..., the list goes on. All because people don't share machine readable phylogenies 😞
Like macroecology & macroevolution? Want to listen to some cool talks from the comfort of your own office (or couch -- we don't judge!) ? We're still accepting online registrations for #BESMacro2026 , July 15-17. Come join us!
www.eventbrite.co.uk/e/bes-macro-...
Ok, this is cool...
Treemble:
A graphical tool to generate Newick strings from phylogenetic tree images🧪
academic.oup.com/bioinformati...
Treemble is a native desktop application for macOS and Windows and is freely available, with documentation, at treemble.org.
naturepoker
Interesting new tool to extract phylogenies from images (Tremble). It is crazy that this is still something we have to do. doi.org/10.1093/bioi...
Science Magazine
Migratory birds perform extraordinary journeys—but we still don’t fully understand how they do it. #TiiaKärkkäinen, @pablosalmon.bsky.social & @barbarahelm.bsky.social reveal why the field of migration physiology is still wide open for new discoveries
➡️ vist.ly/56fr7
#ornithology
Rosemary Mosco
AbstractSummary. Phylogenetic trees are ubiquitous and central to biology, but most published trees are available only as visual diagrams and not in the ma
Abstract. IQ-TREE (https://iqtree.github.io/) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelih
Background Relationships between species, genes and genomes have been printed as trees for over a century. Whilst this may have been the best format for exchanging and sharing phylogenetic hypotheses during the 20th century, the worldwide web now provides faster and automated ways of transferring and sharing phylogenetic knowledge. However, novel software is needed to defrost these published phylogenies for the 21st century. Results TreeRipper is a simple website for the fully-automated recognition of multifurcating phylogenetic trees ( http://linnaeus.zoology.gla.ac.uk/~jhughes/treeripper/ ). The program accepts a range of input image formats (PNG, JPG/JPEG or GIF). The underlying command line c++ program follows a number of cleaning steps to detect lines, remove node labels, patch-up broken lines and corners and detect line edges. The edge contour is then determined to detect the branch length, tip label positions and the topology of the tree. Optical Character Recognition (OCR) is used to convert the tip labels into text with the freely available tesseract-ocr software. 32% of images meeting the prerequisites for TreeRipper were successfully recognised, the largest tree had 115 leaves. Conclusions Despite the diversity of ways phylogenies have been illustrated making the design of a fully automated tree recognition software difficult, TreeRipper is a step towards automating the digitization of past phylogenies. We also provide a dataset of 100 tree images and associated tree files for training and/or benchmarking future software. TreeRipper is an open source project licensed under the GNU General Public Licence v3.
